Re: [AMBER] NETCDF problem

From: David A Case <>
Date: Fri, 14 Jan 2022 08:13:34 -0500

On Fri, Jan 14, 2022, Björn Karlsson wrote:
>NetCDF error: Input/output error
>write_nc_restart(): Could not open restart
>As far as I can understand this message informs me that the restart file is
>corrupt due to coordinate overflow (this is also confirmed when I convert
>the binary restart-file to a pdb-file and then look at the coordinates for
>diffusing water molecules). My believe was however that the use of binary
>NETCDF-files would prevent this behavior. Can anyone please help me to
>clear out what is happening here.

Your understanding of netcdf format is correct. However, the above message
looks like it is happening when write_nc_restart is called, i.e. when you
are trying to output a new netcdf restart file at the end of your new run.

Check your file names carefully. Unless you set the "-O" flag, amber will
not overwrite an existing file, which could lead to the above error if the
requested restart file already exists. But it could be some other
permissions problem as well.


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Received on Fri Jan 14 2022 - 05:30:02 PST
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